Genetic Variant NM_052903.6:c.2839-55G>T (chr15-23003208-C-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_052903.6(TUBGCP5):c.2839-55G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,516,656 control chromosomes in the GnomAD database, including 20,918 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1594 hom., cov: 32)

Exomes 𝑓: 0.16 ( 19324 hom. )

Consequence

TUBGCP5
NM_052903.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.480

Publications

9 publications found

Variant links:

Genes affected

TUBGCP5 (HGNC:18600): (tubulin gamma complex component 5) Enables microtubule binding activity. Involved in microtubule nucleation. Located in centrosome and cytosol. Part of gamma-tubulin large complex. [provided by Alliance of Genome Resources, Apr 2022]

TUBGCP5 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 15-23003208-C-A is Benign according to our data. Variant chr15-23003208-C-A is described in ClinVar as Benign. ClinVar VariationId is 1180177.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052903.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TUBGCP5	NM_052903.6	MANE Select	c.2839-55G>T	intron	N/A	NP_443135.3
TUBGCP5	NM_001354372.2		c.2842-55G>T	intron	N/A	NP_001341301.1
TUBGCP5	NM_001354373.2		c.2839-55G>T	intron	N/A	NP_001341302.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TUBGCP5	ENST00000615383.5	TSL:1 MANE Select	c.2839-55G>T	intron	N/A	ENSP00000480316.1	Q96RT8-1
TUBGCP5	ENST00000620435.4	TSL:2	c.2839-55G>T	intron	N/A	ENSP00000481853.1	Q96RT8-2
TUBGCP5	ENST00000959740.1		c.2815-55G>T	intron	N/A	ENSP00000629799.1

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

18990

AN:

152010

Hom.:

1594

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0288

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.0993

Gnomad ASJ

AF:

0.121

Gnomad EAS

AF:

0.0470

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.263

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.167

Gnomad OTH

AF:

0.111

GnomAD4 exome

AF:

0.163

AC:

222463

AN:

1364528

Hom.:

19324

AF XY:

0.165

AC XY:

112503

AN XY:

683292

show subpopulations

African (AFR)

AF:

0.0254

AC:

800

AN:

31546

American (AMR)

AF:

0.0783

AC:

3432

AN:

43828

Ashkenazi Jewish (ASJ)

AF:

0.121

AC:

3069

AN:

25368

East Asian (EAS)

AF:

0.0676

AC:

2648

AN:

39174

South Asian (SAS)

AF:

0.206

AC:

17181

AN:

83494

European-Finnish (FIN)

AF:

0.253

AC:

13444

AN:

53132

Middle Eastern (MID)

AF:

0.0644

AC:

359

AN:

5574

European-Non Finnish (NFE)

AF:

0.169

AC:

173235

AN:

1025282

Other (OTH)

AF:

0.145

AC:

8295

AN:

57130

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

8891

17782

26674

35565

44456

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5850

11700

17550

23400

29250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.125

AC:

18989

AN:

152128

Hom.:

1594

Cov.:

AF XY:

0.129

AC XY:

9623

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.0287

AC:

1192

AN:

41522

American (AMR)

AF:

0.0990

AC:

1513

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.121

AC:

420

AN:

3472

East Asian (EAS)

AF:

0.0469

AC:

243

AN:

5184

South Asian (SAS)

AF:

0.213

AC:

1024

AN:

4802

European-Finnish (FIN)

AF:

0.263

AC:

2779

AN:

10570

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.167

AC:

11370

AN:

67984

Other (OTH)

AF:

0.112

AC:

236

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

835

1670

2505

3340

4175

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

216

432

648

864

1080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.152

Hom.:

3966

Bravo

AF:

0.106

Asia WGS

AF:

0.153

AC:

530

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

7.1

(source)

DANN

Benign

0.74

PhyloP100

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over